Rework safeSAM2BAM for > BWA v0.5.x unmapped reads
Rework safeSAM2BAM for > BWA v0.5.x unmapped reads

Drop attempt at filtering out malformed reads for BWA 0.7.4;
add processing of unmapped reads to ensure that these correspond
to the more strict interpreation of the spec used by Picard, GATK
and other tools, but now followed by BWA.

MikkelSchubert/paleomix,MikkelSchubert/paleomix,MikkelSchubert/paleomix